{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:09:00Z","timestamp":1772172540630,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006849","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,24]],"date-time":"2019-04-24T00:00:00Z","timestamp":1556064000000}}],"reference-count":27,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2019,4,12]],"date-time":"2019-04-12T00:00:00Z","timestamp":1555027200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["38619"],"award-info":[{"award-number":["38619"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001117","name":"amfAR, The Foundation for AIDS Research","doi-asserted-by":"publisher","award":["109511-61-RKRL"],"award-info":[{"award-number":["109511-61-RKRL"]}],"id":[{"id":"10.13039\/100001117","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201500017C"],"award-info":[{"award-number":["HHSN272201500017C"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006849","type":"journal-article","created":{"date-parts":[[2019,4,12]],"date-time":"2019-04-12T13:37:45Z","timestamp":1555076265000},"page":"e1006849","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":24,"title":["Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1413-3907","authenticated-orcid":true,"given":"Daniel I. S.","family":"Rosenbloom","sequence":"first","affiliation":[]},{"given":"Peter","family":"Bacchetti","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5619-2767","authenticated-orcid":true,"given":"Mars","family":"Stone","sequence":"additional","affiliation":[]},{"given":"Xutao","family":"Deng","sequence":"additional","affiliation":[]},{"given":"Ronald J.","family":"Bosch","sequence":"additional","affiliation":[]},{"given":"Douglas D.","family":"Richman","sequence":"additional","affiliation":[]},{"given":"Janet D.","family":"Siliciano","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3737-9742","authenticated-orcid":true,"given":"John W.","family":"Mellors","sequence":"additional","affiliation":[]},{"given":"Steven G.","family":"Deeks","sequence":"additional","affiliation":[]},{"given":"Roger G.","family":"Ptak","sequence":"additional","affiliation":[]},{"given":"Rebecca","family":"Hoh","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8324-3694","authenticated-orcid":true,"given":"Sheila M.","family":"Keating","sequence":"additional","affiliation":[]},{"given":"Melanie","family":"Dimapasoc","sequence":"additional","affiliation":[]},{"given":"Marta","family":"Massanella","sequence":"additional","affiliation":[]},{"given":"Jun","family":"Lai","sequence":"additional","affiliation":[]},{"given":"Michele D.","family":"Sobolewski","sequence":"additional","affiliation":[]},{"given":"Deanna A.","family":"Kulpa","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1446-125X","authenticated-orcid":true,"given":"Michael P.","family":"Busch","sequence":"additional","affiliation":[]},{"name":"for the Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,4,12]]},"reference":[{"issue":"5341","key":"ref1","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1126\/science.278.5341.1291","article-title":"Recovery of replication-competent HIV despite prolonged suppression of plasma viremia","volume":"278","author":"JK Wong","year":"1997","journal-title":"Science"},{"issue":"5341","key":"ref2","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1126\/science.278.5341.1295","article-title":"Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy","volume":"278","author":"D Finzi","year":"1997","journal-title":"Science"},{"issue":"24","key":"ref3","doi-asserted-by":"crossref","first-page":"13193","DOI":"10.1073\/pnas.94.24.13193","article-title":"Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy","volume":"94","author":"TW Chun","year":"1997","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"6629","key":"ref4","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/387183a0","article-title":"Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection","volume":"387","author":"TW Chun","year":"1997","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"S134","DOI":"10.1093\/infdis\/jiw648","article-title":"Measuring the Size of the Latent Human Immunodeficiency Virus Reservoir: The Present and Future of Evaluating Eradication Strategies","volume":"215","author":"TJ Henrich","year":"2017","journal-title":"Journal of Infectious Diseases"},{"issue":"11","key":"ref6","doi-asserted-by":"crossref","first-page":"e1002466","DOI":"10.1371\/journal.pmed.1002466","article-title":"The end of HIV: Still a very long way to go, but progress continues","volume":"14","author":"SG Deeks","year":"2017","journal-title":"PLoS Med"},{"issue":"1","key":"ref7","first-page":"215","article-title":"Progress Toward HIV Eradication: Case Reports, Current Efforts, and the Challenges Associated with Cure","volume":"67","author":"AR Martin","year":"2016","journal-title":"Progress Toward HIV Eradication: Case Reports, Current Efforts, and the Challenges Associated with Cure"},{"issue":"2","key":"ref8","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1172\/JCI80567","article-title":"Measuring the latent reservoir in vivo","volume":"126","author":"M Massanella","year":"2016","journal-title":"Journal of Clinical Investigation"},{"issue":"4","key":"ref9","doi-asserted-by":"crossref","first-page":"ofv123","DOI":"10.1093\/ofid\/ofv123","article-title":"Designing and Interpreting Limiting Dilution Assays: General Principles and Applications to the Latent Reservoir for Human Immunodeficiency Virus-1","volume":"2","author":"DIS Rosenbloom","year":"2015","journal-title":"Open forum infectious diseases"},{"issue":"2","key":"ref10","doi-asserted-by":"crossref","first-page":"e1003174","DOI":"10.1371\/journal.ppat.1003174","article-title":"Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies","volume":"9","author":"S Eriksson","year":"2013","journal-title":"PLoS pathogens"},{"issue":"3","key":"ref11","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.cell.2013.09.020","article-title":"Replication-Competent Noninduced Proviruses in the Latent Reservoir Increase Barrier to HIV-1 Cure","volume":"155","author":"YC Ho","year":"2013","journal-title":"Cell"},{"issue":"9","key":"ref12","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1038\/nm.4156","article-title":"Defective proviruses rapidly accumulate during acute HIV-1 infection","volume":"22","author":"KM Bruner","year":"2016","journal-title":"Nature Medicine"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1007\/978-1-4939-3046-3_16","article-title":"Measuring the Frequency of Latent HIV-1 in Resting CD4? T Cells Using a Limiting Dilution Coculture Assay","volume":"1354","author":"GM Laird","year":"2016","journal-title":"Methods in molecular biology (Clifton, NJ)"},{"key":"ref14","first-page":"1343","article-title":"Lognormal and Gamma Mixed Negative Binomial Regression","volume":"2012","author":"M Zhou","year":"2012","journal-title":"Proceedings of the International Conference on Machine Learning"},{"issue":"1-2","key":"ref15","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.jim.2009.06.008","article-title":"ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays","volume":"347","author":"Y Hu","year":"2009","journal-title":"J Immunol Methods"},{"issue":"3","key":"ref16","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1214\/06-BA117A","article-title":"Prior distributions for variance parameters in hierarchical models (comment on article by Browne and Draper)","volume":"1","author":"A Gelman","year":"2006","journal-title":"Bayesian Anal"},{"issue":"4","key":"ref17","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1214\/12-BA730","article-title":"On the half-Cauchy prior for a global scale parameter","volume":"7","author":"NG Polson","year":"2012","journal-title":"Bayesian Analysis"},{"issue":"1","key":"ref18","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v076.i01","article-title":"Stan: A Probabilistic Programming Language","volume":"76","author":"B Carpenter","year":"2017","journal-title":"Journal of Statistical Software"},{"issue":"5","key":"ref19","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1007\/s11222-016-9696-4","article-title":"Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC","volume":"27","author":"A Vehtari","year":"2016","journal-title":"Statistics and computing"},{"key":"ref20","doi-asserted-by":"crossref","DOI":"10.1201\/9781315372495","article-title":"Statistical Rethinking: A Bayesian Course with Examples in R and Stan","author":"R McElreath","year":"2018"},{"issue":"10","key":"ref21","doi-asserted-by":"crossref","first-page":"e463","DOI":"10.1016\/S2352-3018(16)30055-8","article-title":"Combined effect of Vacc-4x, recombinant human granulocyte macrophage colony-stimulating factor vaccination, and romidepsin on the HIV-1 reservoir (REDUC): a single-arm, phase 1B\/2A trial","volume":"3","author":"S Leth","year":"2016","journal-title":"The Lancet HIV"},{"key":"ref22","article-title":"Improved Assays to Measure and Characterize the Inducible HIV Reservoir","author":"M Massanella","year":"2018","journal-title":"EBioMedicine"},{"issue":"9","key":"ref23","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1093\/infdis\/jiv218","article-title":"Precise Quantitation of the Latent HIV-1 Reservoir: Implications for Eradication Strategies","volume":"212","author":"AM Crooks","year":"2015","journal-title":"Journal of Infectious Diseases"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.virol.2017.05.008","article-title":"Relative efficacy of T cell stimuli as inducers of productive HIV-1 replication in latently infected CD4 lymphocytes from patients on suppressive cART","volume":"508","author":"N Beliakova-Bethell","year":"2017","journal-title":"Virology"},{"issue":"11","key":"ref25","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1373\/clinchem.2015.243287","article-title":"Rapid, Fully Automated Digital Immunoassay for p24 Protein with the Sensitivity of Nucleic Acid Amplification for Detecting Acute HIV Infection","volume":"61","author":"C Cabrera","year":"2015","journal-title":"Clinical Chemistry"},{"issue":"87","key":"ref26","doi-asserted-by":"crossref","first-page":"87ps24","DOI":"10.1126\/scitranslmed.3001628","article-title":"Breaking Free of Sample Size Dogma to Perform Innovative Translational Research","volume":"3","author":"P Bacchetti","year":"2011","journal-title":"Science Translational Medicine"},{"issue":"S5","key":"ref27","first-page":"1","article-title":"Next generation viral outgrowth assays as proxies for classic QVOA to measure HIV-1 reservoir size","volume":"3","author":"M Stone","year":"2017","journal-title":"Journal of Virus Eradication"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006849","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,24]],"date-time":"2019-04-24T00:00:00Z","timestamp":1556064000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006849","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T05:27:59Z","timestamp":1589002079000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006849"}},"subtitle":[],"editor":[{"given":"Roland R","family":"Regoes","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,4,12]]},"references-count":27,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,4,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006849","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/329672","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,12]]}}}